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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgtctatccttttcatgctccttcgttttggacttccattttgtctgtatgtatgaagagcatccacgcgatagtgattgcttgatccgtgtt...

Basic information

species Selaginella moellendorffii
transcript EFJ08380
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08380 (Selaginella moellendorffii), 5'ss of exon 19
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgtctatccttttcatgctccttcgttttggacttccattttgtc-tgtatgtatgaagagcatccacgcgatagtgattgcttgatccgtgtt
 ||| | || || ||||||||||| ||||| ||||| |||||||| || ||||| ||||||||||  || ||  | ||    || |||| | | ||||| ||    || |  |  |    | | || ||||  ||   ||    ||||  || |  | || |  |     |        | |                   
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttc-ttcattaaatcaaaacct-ctgcttcacttcacacaataatttactcattcaagttttgattcttttttttttgtggcag----------------

upper sequence: EFJ08380 (Selaginella moellendorffii), 5'ss of exon 19
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 20
TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgta---agctcgtctatccttttcat-gctccttcgttttggacttccattttgt-ctgtatgtatgaagagcatccacgcg-atagtgattgcttgatccgtgtt---------
 ||  |||| ||||| || ||||||||||| |||||||||||||| ||| |||| |||||||| |  ||  |  | ||    ||||| |   | || || |||   |      |    ||    || |   ||||  ||||  |   ||| |    | |||         |   || |     ||      |||     || | |          
ACAGCGGGATCCGCTTATTGAGTACAAGCTTGAAGGCTACAATCTATTCTTGGAGATGATGGCACAGATAAGAAGAAATGTTATTTATTCAATATACCAGgtatatattaaaccagagctagatattgtatcttcagtttgtgcacacatgtcacacagtacactcaccaattctctatttttatctcacctgcaatgcccttttcctatggcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169087117|gb|FE495170.1|FE495170
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169071799|gb|FE477163.1|FE477163
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169076023|gb|FE481005.1|FE481005
EST:     GGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATNCA-                         TTCA-GCCAGTGATGATC
genomic: GGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTAT-CAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATC
EST: gi|169028805|gb|FE438036.1|FE438036
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169041941|gb|FE448459.1|FE448459
EST:     CGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: CGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169076022|gb|FE481004.1|FE481004
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169062412|gb|FE469471.1|FE469471
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCA-GCCAGTGATGATCGACAA
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAA
EST: gi|169097496|gb|FE497938.1|FE497938
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169029747|gb|FE440993.1|FE440993
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169083538|gb|FE491410.1|FE491410
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169076626|gb|FE484733.1|FE484733
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169071798|gb|FE477162.1|FE477162
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169070007|gb|FE476476.1|FE476476
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCGACAA-GAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG
EST: gi|169082408|gb|FE489581.1|FE489581
EST:     TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAA                         TTCAAGCCAGTGATGATCTACAAAGAAACACTGGATCGATCGAAGAGCACG
genomic: TGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 32 (upstream exon), 35 (downstream exon)
Score: 22

TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgt ... tttgcatcagTTCAAGCCAGTGATGATCGACAAAGAAACACTGGATCGATCGAAGAGCACGAAAAACGGGAAAACTGCTGCCACAGTCTGATGAGAAATAGGTGCACAGG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAGGGACCCGCTCATCGAGTACAAGCTAGAAGGCTACAATCTTTTCCTGGACATGATGGCTCGTATCCGTCGCAACACCATTTACTGCGTCTATCAAgtaagctcgtctatccttttcatgctccttcgttttggacttccattttgtctgtatgtatgaagagcatccacgcgatagtgattgcttgatccgtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcttg